Correlation between copy number variations of arm-level result and molecular subtypes
Adrenocortical Carcinoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C19P30MZ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C19P30MZ
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 82 arm-level events and 10 molecular subtypes across 90 patients, 211 significant findings detected with P value < 0.05 and Q value < 0.25.

- 1q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

- 2p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 2q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 4p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 4q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 5q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 6p gain cnv correlated to 'CN_CNMF'.

- 7p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 7q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 8p gain cnv correlated to 'CN_CNMF'.

- 8q gain cnv correlated to 'CN_CNMF'.

- 9p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 9q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

- 10p gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

- 10q gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- 11q gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.

- 12p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 12q gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 13q gain cnv correlated to 'MRNASEQ_CNMF'.

- 14q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 15q gain cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 16p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 16q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 17q gain cnv correlated to 'CN_CNMF'.

- 19p gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 19q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 20p gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 20q gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 21q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- xp gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- xq gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 1p loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

- 1q loss cnv correlated to 'RPPA_CHIERARCHICAL'.

- 2p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

- 2q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.

- 3q loss cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 4p loss cnv correlated to 'MRNASEQ_CNMF'.

- 4q loss cnv correlated to 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 5p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 8p loss cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 8q loss cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

- 9p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- 9q loss cnv correlated to 'RPPA_CHIERARCHICAL'.

- 11p loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 11q loss cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

- 12p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 12q loss cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

- 13q loss cnv correlated to 'CN_CNMF'.

- 14q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- 15q loss cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

- 16p loss cnv correlated to 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

- 16q loss cnv correlated to 'MIRSEQ_MATURE_CNMF'.

- 17p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

- 17q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

- 18p loss cnv correlated to 'CN_CNMF'.

- 18q loss cnv correlated to 'CN_CNMF'.

- 19p loss cnv correlated to 'MRNASEQ_CHIERARCHICAL'.

- 20p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

- 22q loss cnv correlated to 'CN_CNMF'.

- xp loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

- xq loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 211 significant findings detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
14q gain | 21 (23%) | 69 | 0.0148 (0.0882) | 0.0584 (0.207) | 0.0247 (0.122) | 0.43 (0.663) | 0.00045 (0.00683) | 0.00109 (0.0135) | 1e-05 (0.00039) | 0.00017 (0.00317) | 6e-05 (0.00154) | 1e-05 (0.00039)
16p gain | 49 (54%) | 41 | 1e-05 (0.00039) | 0.0107 (0.0752) | 1 (1.00) | 0.038 (0.159) | 1e-05 (0.00039) | 1e-05 (0.00039) | 0.0451 (0.181) | 0.026 (0.127) | 0.0293 (0.135) | 0.276 (0.5)
20p gain | 46 (51%) | 44 | 1e-05 (0.00039) | 0.235 (0.46) | 0.00265 (0.0265) | 0.00853 (0.0636) | 0.00017 (0.00317) | 0.0001 (0.00222) | 0.00488 (0.0414) | 0.0892 (0.266) | 0.00945 (0.0686) | 0.00408 (0.0372)
16q gain | 47 (52%) | 43 | 1e-05 (0.00039) | 0.00792 (0.0601) | 1 (1.00) | 0.322 (0.549) | 0.00011 (0.00237) | 1e-05 (0.00039) | 0.0245 (0.122) | 0.013 (0.0847) | 0.0141 (0.0873) | 0.46 (0.691)
20q gain | 49 (54%) | 41 | 1e-05 (0.00039) | 0.0658 (0.226) | 0.0157 (0.0918) | 0.0759 (0.245) | 7e-05 (0.00174) | 0.00031 (0.00508) | 0.0187 (0.103) | 0.277 (0.5) | 0.0115 (0.0776) | 0.0145 (0.0874)
21q gain | 31 (34%) | 59 | 0.0213 (0.112) | 0.00789 (0.0601) | 0.121 (0.318) | 0.235 (0.46) | 0.0187 (0.103) | 0.00101 (0.0129) | 0.0134 (0.0852) | 0.0204 (0.109) | 0.0029 (0.0273) | 0.0841 (0.255)
2q gain | 12 (13%) | 78 | 0.0527 (0.197) | 0.00235 (0.0238) | 1 (1.00) | 0.174 (0.394) | 0.0183 (0.103) | 0.00285 (0.0273) | 0.0539 (0.198) | 0.00495 (0.0414) | 0.0209 (0.11) | 0.0237 (0.12)
9q gain | 29 (32%) | 61 | 0.00033 (0.00531) | 0.00102 (0.0129) | 0.00425 (0.038) | 0.0693 (0.23) | 0.0242 (0.122) | 0.00185 (0.02) | 0.034 (0.151) | 0.35 (0.575) | 0.089 (0.266) | 0.0841 (0.255)
10p gain | 25 (28%) | 65 | 0.002 (0.0211) | 0.0591 (0.209) | 0.0284 (0.133) | 0.0142 (0.0873) | 4e-05 (0.00113) | 0.00022 (0.00384) | 0.0343 (0.151) | 0.509 (0.719) | 0.0552 (0.199) | 0.453 (0.683)
10q gain | 26 (29%) | 64 | 0.00156 (0.0173) | 0.0709 (0.234) | 0.0549 (0.198) | 0.0143 (0.0873) | 3e-05 (0.000946) | 0.00045 (0.00683) | 0.0205 (0.109) | 0.344 (0.567) | 0.0299 (0.136) | 0.846 (0.989)
9p loss | 20 (22%) | 70 | 0.00165 (0.018) | 0.0475 (0.186) | 0.101 (0.288) | 0.116 (0.312) | 0.0001 (0.00222) | 0.00102 (0.0129) | 0.00931 (0.0682) | 0.14 (0.347) | 0.00431 (0.038) | 0.936 (1.00)
17p loss | 32 (36%) | 58 | 0.00278 (0.0273) | 0.00018 (0.00321) | 0.342 (0.567) | 0.194 (0.417) | 0.0111 (0.0763) | 0.0136 (0.086) | 0.0807 (0.252) | 0.0028 (0.0273) | 0.0132 (0.0852) | 0.115 (0.311)
2p gain | 13 (14%) | 77 | 0.00732 (0.0572) | 0.0013 (0.015) | 0.193 (0.416) | 0.342 (0.567) | 0.012 (0.0797) | 0.00026 (0.00444) | 0.372 (0.599) | 0.0187 (0.103) | 0.127 (0.326) | 0.0724 (0.238)
4p gain | 37 (41%) | 53 | 1e-05 (0.00039) | 0.0446 (0.18) | 0.769 (0.929) | 0.466 (0.691) | 1e-05 (0.00039) | 5e-05 (0.00137) | 0.293 (0.516) | 0.00201 (0.0211) | 0.343 (0.567) | 0.862 (1)
4q gain | 33 (37%) | 57 | 2e-05 (0.000656) | 0.0374 (0.159) | 1 (1.00) | 0.729 (0.89) | 2e-05 (0.000656) | 1e-05 (0.00039) | 0.557 (0.753) | 0.00083 (0.0112) | 0.359 (0.586) | 0.95 (1.00)
5p gain | 57 (63%) | 33 | 1e-05 (0.00039) | 0.037 (0.159) | 0.0682 (0.227) | 0.0325 (0.146) | 0.00051 (0.00734) | 1e-05 (0.00039) | 0.252 (0.472) | 0.226 (0.454) | 0.0744 (0.243) | 0.357 (0.583)
9p gain | 20 (22%) | 70 | 8e-05 (0.00193) | 0.00217 (0.0222) | 0.0115 (0.0776) | 0.135 (0.342) | 0.00957 (0.0688) | 0.0112 (0.0769) | 0.386 (0.621) | 0.551 (0.752) | 0.464 (0.691) | 0.251 (0.472)
8q loss | 12 (13%) | 78 | 0.00484 (0.0414) | 0.087 (0.262) | 0.422 (0.657) | 0.0356 (0.155) | 0.0324 (0.146) | 0.124 (0.324) | 0.0765 (0.246) | 0.0342 (0.151) | 0.182 (0.404) | 0.0375 (0.159)
16p loss | 6 (7%) | 84 | 0.126 (0.324) | 0.0503 (0.194) | 1 (1.00) | 0.0469 (0.185) | 0.00214 (0.0222) | 0.00431 (0.038) | 0.013 (0.0847) | 0.443 (0.675) | 0.00029 (0.00485) | 0.468 (0.691)
5q gain | 53 (59%) | 37 | 1e-05 (0.00039) | 0.00836 (0.0629) | 0.533 (0.734) | 0.147 (0.351) | 0.0005 (0.00732) | 1e-05 (0.00039) | 0.334 (0.561) | 0.138 (0.346) | 0.21 (0.438) | 0.17 (0.389)
12q gain | 64 (71%) | 26 | 1e-05 (0.00039) | 0.309 (0.535) | 0.503 (0.715) | 0.0281 (0.133) | 0.00057 (0.00792) | 0.00012 (0.00246) | 0.235 (0.46) | 0.454 (0.683) | 0.219 (0.448) | 0.591 (0.796)
15q gain | 11 (12%) | 79 | 0.0945 (0.275) | 0.0462 (0.184) | 0.193 (0.416) | 0.845 (0.989) | 0.011 (0.0762) | 0.00545 (0.0438) | 0.363 (0.59) | 0.00059 (0.00806) | 0.504 (0.715) | 0.255 (0.475)
19p gain | 56 (62%) | 34 | 0.00373 (0.0344) | 0.054 (0.198) | 0.196 (0.419) | 0.0189 (0.103) | 0.00122 (0.0145) | 0.00048 (0.00716) | 0.468 (0.691) | 0.47 (0.691) | 0.638 (0.832) | 0.216 (0.447)
19q gain | 52 (58%) | 38 | 6e-05 (0.00154) | 0.05 (0.194) | 0.552 (0.752) | 0.0563 (0.202) | 0.00036 (0.00568) | 0.00102 (0.0129) | 0.143 (0.347) | 0.112 (0.309) | 0.519 (0.728) | 0.12 (0.317)
xp gain | 42 (47%) | 48 | 1e-05 (0.00039) | 0.242 (0.465) | 1 (1.00) | 0.0299 (0.136) | 0.0011 (0.0135) | 0.00536 (0.0435) | 1 (1.00) | 0.0824 (0.254) | 0.427 (0.662) | 0.218 (0.448)
xq gain | 41 (46%) | 49 | 2e-05 (0.000656) | 0.165 (0.382) | 0.767 (0.929) | 0.0438 (0.178) | 0.00128 (0.015) | 0.00877 (0.0648) | 0.795 (0.947) | 0.15 (0.355) | 0.343 (0.567) | 0.139 (0.346)
8p loss | 16 (18%) | 74 | 0.00535 (0.0435) | 0.224 (0.453) | 0.143 (0.347) | 0.00053 (0.00749) | 0.18 (0.403) | 0.141 (0.347) | 0.179 (0.401) | 0.0238 (0.12) | 0.257 (0.476) | 0.0292 (0.135)
17q loss | 24 (27%) | 66 | 0.015 (0.0885) | 0.00483 (0.0414) | 0.121 (0.318) | 0.518 (0.727) | 0.118 (0.313) | 0.0329 (0.147) | 0.0677 (0.227) | 0.0205 (0.109) | 0.227 (0.455) | 0.106 (0.3)
7p gain | 48 (53%) | 42 | 1e-05 (0.00039) | 0.117 (0.313) | 0.533 (0.734) | 0.0914 (0.27) | 0.00016 (0.00312) | 0.00152 (0.0171) | 0.915 (1.00) | 0.551 (0.752) | 0.275 (0.5) | 0.288 (0.512)
7q gain | 48 (53%) | 42 | 2e-05 (0.000656) | 0.116 (0.312) | 0.533 (0.734) | 0.243 (0.465) | 1e-05 (0.00039) | 0.00012 (0.00246) | 0.916 (1.00) | 0.328 (0.556) | 0.276 (0.5) | 0.191 (0.414)
12p gain | 64 (71%) | 26 | 1e-05 (0.00039) | 0.208 (0.436) | 0.528 (0.734) | 0.0676 (0.227) | 0.00014 (0.0028) | 0.0001 (0.00222) | 0.248 (0.472) | 0.21 (0.438) | 0.129 (0.33) | 0.251 (0.472)
2p loss | 17 (19%) | 73 | 0.00684 (0.0539) | 0.0276 (0.132) | 1 (1.00) | 0.66 (0.848) | 0.613 (0.815) | 0.27 (0.494) | 0.0381 (0.159) | 0.769 (0.929) | 0.228 (0.456) | 0.7 (0.87)
2q loss | 15 (17%) | 75 | 0.00495 (0.0414) | 0.00112 (0.0135) | 1 (1.00) | 0.884 (1.00) | 0.113 (0.31) | 0.0539 (0.198) | 0.0314 (0.142) | 0.728 (0.89) | 0.071 (0.234) | 0.533 (0.734)
4q loss | 11 (12%) | 79 | 0.24 (0.463) | 0.0964 (0.278) | 0.67 (0.858) | 0.923 (1.00) | 0.00756 (0.0585) | 0.0267 (0.13) | 0.25 (0.472) | 0.813 (0.963) | 0.0134 (0.0852) | 0.905 (1.00)
14q loss | 18 (20%) | 72 | 0.0271 (0.131) | 0.447 (0.677) | 0.476 (0.696) | 0.0543 (0.198) | 0.0176 (0.0994) | 0.0469 (0.185) | 0.41 (0.646) | 0.527 (0.734) | 0.218 (0.448) | 0.147 (0.351)
xp loss | 16 (18%) | 74 | 4e-05 (0.00113) | 0.395 (0.628) | 0.252 (0.472) | 0.0949 (0.275) | 0.023 (0.118) | 0.0282 (0.133) | 0.694 (0.868) | 0.0894 (0.266) | 0.156 (0.365) | 1 (1.00)
xq loss | 15 (17%) | 75 | 0.00286 (0.0273) | 0.152 (0.356) | 0.051 (0.194) | 0.0941 (0.275) | 0.0176 (0.0994) | 0.0165 (0.0961) | 0.503 (0.715) | 0.173 (0.394) | 0.184 (0.405) | 0.624 (0.822)
1q gain | 8 (9%) | 82 | 0.0422 (0.174) | 0.655 (0.847) | 0.326 (0.553) | 0.557 (0.753) | 0.0457 (0.183) | 0.0782 (0.249) | 0.0647 (0.223) | 0.243 (0.465) | 0.147 (0.351) | 0.851 (0.992)
11q gain | 6 (7%) | 84 | 0.124 (0.324) | 0.174 (0.394) | 0.611 (0.815) | 0.484 (0.705) | 0.0437 (0.178) | 0.0772 (0.246) | 0.186 (0.407) | 0.368 (0.597) | 0.00533 (0.0435) | 0.391 (0.625)
3q loss | 20 (22%) | 70 | 0.166 (0.383) | 0.165 (0.382) | 0.143 (0.347) | 0.602 (0.808) | 0.0226 (0.118) | 0.0294 (0.135) | 0.193 (0.416) | 0.341 (0.567) | 0.315 (0.541) | 0.116 (0.312)
11p loss | 24 (27%) | 66 | 0.00649 (0.0517) | 0.0173 (0.0994) | 1 (1.00) | 0.798 (0.948) | 0.22 (0.448) | 0.189 (0.413) | 0.282 (0.506) | 0.891 (1.00) | 0.693 (0.868) | 1 (1.00)
11q loss | 23 (26%) | 67 | 0.012 (0.0797) | 0.00308 (0.0287) | 0.729 (0.89) | 0.395 (0.628) | 0.136 (0.343) | 0.126 (0.324) | 0.107 (0.301) | 0.827 (0.973) | 0.489 (0.707) | 0.781 (0.936)
12q loss | 4 (4%) | 86 | 0.185 (0.406) | 0.0498 (0.194) | 1 (1.00) | 0.0828 (0.254) | 0.446 (0.677) | 0.00999 (0.0709) | 0.329 (0.556) | 0.24 (0.463) | 0.677 (0.866) | 0.115 (0.311)
20p loss | 9 (10%) | 81 | 0.0425 (0.174) | 0.306 (0.531) | 0.0514 (0.194) | 0.854 (0.993) | 0.212 (0.44) | 0.125 (0.324) | 0.068 (0.227) | 0.449 (0.68) | 0.0202 (0.109) | 0.441 (0.674)
6p gain | 18 (20%) | 72 | 0.0175 (0.0994) | 0.683 (0.868) | 0.469 (0.691) | 0.874 (1.00) | 0.0668 (0.227) | 0.472 (0.693) | 0.163 (0.378) | 0.0544 (0.198) | 0.415 (0.649) | 0.233 (0.46)
8p gain | 32 (36%) | 58 | 4e-05 (0.00113) | 0.141 (0.347) | 0.196 (0.419) | 0.438 (0.673) | 0.168 (0.385) | 0.147 (0.351) | 0.112 (0.309) | 0.173 (0.394) | 0.243 (0.465) | 0.516 (0.727)
8q gain | 38 (42%) | 52 | 0.00018 (0.00321) | 0.293 (0.516) | 0.369 (0.597) | 0.468 (0.691) | 0.412 (0.648) | 0.233 (0.46) | 0.499 (0.713) | 0.261 (0.482) | 0.523 (0.731) | 0.645 (0.839)
13q gain | 6 (7%) | 84 | 0.402 (0.636) | 0.463 (0.691) | 0.611 (0.815) | 0.723 (0.889) | 0.0398 (0.166) | 0.639 (0.832) | 0.143 (0.347) | 0.915 (1.00) | 0.181 (0.404) | 0.699 (0.87)
17q gain | 7 (8%) | 83 | 0.0244 (0.122) | 0.341 (0.567) | 0.491 (0.707) |  | 0.688 (0.868) | 0.143 (0.347) | 0.208 (0.436) | 0.794 (0.947) | 0.0607 (0.213) | 0.0606 (0.213)
1p loss | 29 (32%) | 61 | 0.118 (0.313) | 0.144 (0.348) | 0.533 (0.734) | 0.129 (0.33) | 0.44 (0.674) | 0.0664 (0.227) | 0.471 (0.692) | 0.409 (0.645) | 0.0273 (0.131) | 0.948 (1.00)
1q loss | 20 (22%) | 70 | 0.206 (0.436) | 0.0885 (0.266) | 1 (1.00) | 0.0251 (0.123) | 0.962 (1.00) | 0.601 (0.808) | 0.37 (0.597) | 0.841 (0.986) | 0.0772 (0.246) | 0.49 (0.707)
4p loss | 10 (11%) | 80 | 0.0964 (0.278) | 0.237 (0.461) | 1 (1.00) | 0.989 (1.00) | 0.0227 (0.118) | 0.0806 (0.252) | 0.312 (0.538) | 0.932 (1.00) | 0.0515 (0.194) | 1 (1.00)
5p loss | 8 (9%) | 82 | 0.288 (0.512) | 0.0514 (0.194) | 1 (1.00) | 0.191 (0.414) | 0.229 (0.457) | 0.01 (0.0709) | 0.771 (0.93) | 0.297 (0.52) | 0.696 (0.868) | 1 (1.00)
9q loss | 11 (12%) | 79 | 0.325 (0.553) | 0.934 (1.00) | 1 (1.00) | 0.0369 (0.159) | 0.0794 (0.251) | 0.321 (0.549) | 0.557 (0.753) | 0.494 (0.709) | 0.215 (0.445) | 0.807 (0.957)
12p loss | 5 (6%) | 85 | 0.0926 (0.271) | 0.254 (0.474) | 1 (1.00) | 0.0825 (0.254) | 0.619 (0.821) | 0.0377 (0.159) | 0.103 (0.291) | 0.518 (0.727) | 0.427 (0.662) | 0.151 (0.355)
13q loss | 39 (43%) | 51 | 0.0143 (0.0873) | 0.0817 (0.254) | 0.759 (0.922) | 0.944 (1.00) | 0.626 (0.822) | 0.885 (1.00) | 0.753 (0.916) | 0.305 (0.531) | 0.613 (0.815) | 0.495 (0.709)
15q loss | 21 (23%) | 69 | 0.0804 (0.252) | 0.418 (0.652) | 0.713 (0.879) | 0.509 (0.719) | 0.11 (0.307) | 0.231 (0.459) | 0.608 (0.814) | 0.0401 (0.166) | 0.289 (0.514) | 0.875 (1.00)
16q loss | 5 (6%) | 85 | 0.218 (0.448) | 0.0759 (0.245) | 0.611 (0.815) | 0.176 (0.396) | 0.057 (0.203) | 0.0855 (0.259) | 0.169 (0.386) | 0.306 (0.531) | 0.00152 (0.0171) | 0.699 (0.87)
18p loss | 37 (41%) | 53 | 0.0237 (0.12) | 0.265 (0.486) | 0.55 (0.752) | 0.69 (0.868) | 0.776 (0.933) | 0.646 (0.839) | 0.694 (0.868) | 0.694 (0.868) | 0.354 (0.58) | 0.345 (0.567)
18q loss | 35 (39%) | 55 | 0.0362 (0.157) | 0.425 (0.661) | 0.764 (0.926) | 0.534 (0.734) | 0.824 (0.972) | 0.935 (1.00) | 0.496 (0.71) | 0.914 (1.00) | 0.291 (0.516) | 0.353 (0.579)
19p loss | 5 (6%) | 85 | 0.0926 (0.271) | 0.441 (0.674) | 0.467 (0.691) |  | 0.158 (0.368) | 0.0144 (0.0873) | 0.14 (0.347) | 0.718 (0.884) | 0.28 (0.504) | 0.111 (0.309)
22q loss | 48 (53%) | 42 | 0.0146 (0.0874) | 0.0809 (0.252) | 0.555 (0.753) | 0.481 (0.702) | 0.62 (0.821) | 0.283 (0.507) | 0.874 (1.00) | 0.825 (0.972) | 0.682 (0.868) | 0.224 (0.453)
1p gain | 4 (4%) | 86 | 0.184 (0.405) |  | 0.467 (0.691) |  |  |  |  |  |  |
3p gain | 13 (14%) | 77 | 0.283 (0.507) | 0.068 (0.227) | 0.443 (0.675) | 0.88 (1.00) | 0.332 (0.558) | 0.365 (0.593) | 0.408 (0.644) | 0.108 (0.303) | 0.634 (0.828) | 0.388 (0.622)
3q gain | 15 (17%) | 75 | 0.401 (0.636) | 0.0514 (0.194) | 0.476 (0.696) | 0.821 (0.97) | 0.0529 (0.197) | 0.792 (0.947) | 0.651 (0.843) | 0.245 (0.468) | 0.68 (0.868) | 0.711 (0.878)
6q gain | 16 (18%) | 74 | 0.0747 (0.243) | 0.454 (0.683) | 1 (1.00) | 0.685 (0.868) | 0.199 (0.424) | 0.294 (0.516) | 0.299 (0.523) | 0.197 (0.42) | 0.151 (0.355) | 0.437 (0.672)
11p gain | 5 (6%) | 85 | 0.0912 (0.27) |  | 1 (1.00) |  |  |  |  |  |  |
17p gain | 5 (6%) | 85 | 0.113 (0.31) | 0.339 (0.567) | 0.491 (0.707) |  | 0.686 (0.868) | 0.143 (0.347) | 0.207 (0.436) | 0.795 (0.947) | 0.0615 (0.215) | 0.0627 (0.218)
18p gain | 6 (7%) | 84 | 0.263 (0.484) |  | 0.491 (0.707) |  |  |  |  |  |  |
18q gain | 5 (6%) | 85 | 0.493 (0.709) |  | 1 (1.00) |  |  |  |  |  |  |
22q gain | 3 (3%) | 87 | 0.632 (0.827) |  | 0.467 (0.691) |  |  |  |  |  |  |
3p loss | 20 (22%) | 70 | 0.257 (0.476) | 0.144 (0.348) | 0.252 (0.472) | 0.292 (0.516) | 0.111 (0.309) | 0.136 (0.343) | 0.523 (0.731) | 0.39 (0.625) | 0.684 (0.868) | 0.314 (0.54)
5q loss | 7 (8%) | 83 | 0.897 (1.00) | 0.657 (0.847) | 1 (1.00) |  | 0.276 (0.5) | 0.136 (0.343) | 0.658 (0.847) | 0.126 (0.324) | 0.66 (0.848) | 0.85 (0.992)
6p loss | 19 (21%) | 71 | 0.148 (0.352) | 0.851 (0.992) | 1 (1.00) | 0.234 (0.46) | 0.624 (0.822) | 0.688 (0.868) | 0.626 (0.822) | 0.0988 (0.283) | 0.728 (0.89) | 0.524 (0.731)
6q loss | 22 (24%) | 68 | 0.0632 (0.219) | 0.861 (1) | 0.503 (0.715) | 0.271 (0.495) | 0.634 (0.828) | 0.692 (0.868) | 0.729 (0.89) | 0.175 (0.394) | 0.556 (0.753) | 0.321 (0.549)
7p loss | 5 (6%) | 85 | 0.393 (0.626) | 0.585 (0.789) | 0.236 (0.46) | 0.206 (0.436) | 0.911 (1.00) | 0.891 (1.00) | 0.815 (0.965) | 0.414 (0.649) | 0.834 (0.98) | 0.115 (0.311)
7q loss | 6 (7%) | 84 | 0.314 (0.54) | 0.303 (0.529) | 0.236 (0.46) | 0.781 (0.936) | 0.62 (0.821) | 0.656 (0.847) | 1 (1.00) | 0.234 (0.46) | 0.733 (0.893) | 0.151 (0.355)
10p loss | 12 (13%) | 78 | 0.225 (0.453) | 0.429 (0.663) | 1 (1.00) | 0.0547 (0.198) | 0.267 (0.489) | 1 (1.00) | 0.683 (0.868) | 0.708 (0.876) | 1 (1.00) | 0.33 (0.557)
10q loss | 10 (11%) | 80 | 0.538 (0.738) | 0.628 (0.824) | 1 (1.00) | 0.238 (0.462) | 0.535 (0.734) | 1 (1.00) | 1 (1.00) | 0.706 (0.876) | 1 (1.00) | 0.287 (0.512)
19q loss | 4 (4%) | 86 | 0.184 (0.405) | 0.708 (0.876) | 1 (1.00) |  | 0.773 (0.931) | 0.118 (0.313) | 0.785 (0.94) | 0.207 (0.436) | 1 (1.00) | 0.432 (0.666)
20q loss | 3 (3%) | 87 | 0.182 (0.404) |  | 0.491 (0.707) |  |  |  |  |  |  |
21q loss | 15 (17%) | 75 | 0.115 (0.311) | 0.338 (0.566) | 0.225 (0.453) | 0.0527 (0.197) | 0.257 (0.476) | 0.252 (0.472) | 0.223 (0.453) | 0.51 (0.719) | 0.0829 (0.254) | 0.101 (0.287)

'1q gain' versus 'CN_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.17

Table S1. Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
1Q GAIN MUTATED | 7 | 0 | 1 | 0
1Q GAIN WILD-TYPE | 29 | 26 | 15 | 12

Figure S1. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.0457 (Fisher's exact test), Q value = 0.18

Table S2. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
1Q GAIN MUTATED | 4 | 2 | 0 | 0
1Q GAIN WILD-TYPE | 20 | 11 | 17 | 23

Figure S2. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'CN_CNMF'

P value = 0.00732 (Fisher's exact test), Q value = 0.057

Table S3. Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
2P GAIN MUTATED | 11 | 1 | 1 | 0
2P GAIN WILD-TYPE | 25 | 25 | 15 | 12

Figure S3. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.015

Table S4. Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
2P GAIN MUTATED | 7 | 1 | 0 | 1 | 0
2P GAIN WILD-TYPE | 11 | 10 | 20 | 17 | 11

Figure S4. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.08

Table S5. Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
2P GAIN MUTATED | 7 | 0 | 0 | 2
2P GAIN WILD-TYPE | 17 | 13 | 17 | 21

Figure S5. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0044

Table S6. Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
2P GAIN MUTATED | 8 | 0 | 1 | 0
2P GAIN WILD-TYPE | 15 | 23 | 6 | 24

Figure S6. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.1

Table S7. Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
2P GAIN MUTATED | 0 | 1 | 1 | 6 | 1
2P GAIN WILD-TYPE | 16 | 26 | 10 | 14 | 3

Figure S7. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.024

Table S8. Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
2Q GAIN MUTATED | 6 | 0 | 0 | 1 | 0
2Q GAIN WILD-TYPE | 12 | 11 | 20 | 17 | 11

Figure S8. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 0.0183 (Fisher's exact test), Q value = 0.1

Table S9. Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
2Q GAIN MUTATED | 6 | 0 | 0 | 1
2Q GAIN WILD-TYPE | 18 | 13 | 17 | 22

Figure S9. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00285 (Fisher's exact test), Q value = 0.027

Table S10. Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
2Q GAIN MUTATED | 6 | 0 | 1 | 0
2Q GAIN WILD-TYPE | 17 | 23 | 6 | 24

Figure S10. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00495 (Fisher's exact test), Q value = 0.041

Table S11. Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
2Q GAIN MUTATED | 0 | 0 | 1 | 6 | 0
2Q GAIN WILD-TYPE | 16 | 27 | 10 | 14 | 4

Figure S11. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.11

Table S12. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
2Q GAIN MUTATED | 2 | 5 | 0
2Q GAIN WILD-TYPE | 26 | 17 | 27

Figure S12. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.12

Table S13. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 39 | 24 | 14
2Q GAIN MUTATED | 7 | 0 | 0
2Q GAIN WILD-TYPE | 32 | 24 | 14

Figure S13. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S14. Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
4P GAIN MUTATED | 4 | 13 | 12 | 8
4P GAIN WILD-TYPE | 32 | 13 | 4 | 4

Figure S14. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.18

Table S15. Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
4P GAIN MUTATED | 3 | 4 | 13 | 6 | 5
4P GAIN WILD-TYPE | 15 | 7 | 7 | 12 | 6

Figure S15. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S16. Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
4P GAIN MUTATED | 1 | 8 | 11 | 10
4P GAIN WILD-TYPE | 23 | 5 | 6 | 13

Figure S16. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0014

Table S17. Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
4P GAIN MUTATED | 2 | 15 | 0 | 13
4P GAIN WILD-TYPE | 21 | 8 | 7 | 11

Figure S17. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00201 (Fisher's exact test), Q value = 0.021

Table S18. Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
4P GAIN MUTATED | 11 | 10 | 5 | 2 | 3
4P GAIN WILD-TYPE | 5 | 17 | 6 | 18 | 1

Figure S18. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00066

Table S19. Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
4Q GAIN MUTATED | 3 | 12 | 11 | 7
4Q GAIN WILD-TYPE | 33 | 14 | 5 | 5

Figure S19. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.16

Table S20. Gene #8: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
4Q GAIN MUTATED | 2 | 4 | 12 | 6 | 4
4Q GAIN WILD-TYPE | 16 | 7 | 8 | 12 | 7

Figure S20. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00066

Table S21. Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
4Q GAIN MUTATED | 0 | 8 | 9 | 10
4Q GAIN WILD-TYPE | 24 | 5 | 8 | 13

Figure S21. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S22. Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
4Q GAIN MUTATED | 1 | 15 | 0 | 11
4Q GAIN WILD-TYPE | 22 | 8 | 7 | 13

Figure S22. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.011

Table S23. Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
4Q GAIN MUTATED | 10 | 9 | 5 | 1 | 3
4Q GAIN WILD-TYPE | 6 | 18 | 6 | 19 | 1

Figure S23. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S24. Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
5P GAIN MUTATED | 10 | 24 | 14 | 9
5P GAIN WILD-TYPE | 26 | 2 | 2 | 3

Figure S24. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #1: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.16

Table S25. Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
5P GAIN MUTATED | 7 | 5 | 15 | 14 | 9
5P GAIN WILD-TYPE | 11 | 6 | 5 | 4 | 2

Figure S25. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0325 (Fisher's exact test), Q value = 0.15

Table S26. Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
5P GAIN MUTATED | 4 | 5 | 6 | 1 | 4 | 4 | 5 | 1
5P GAIN WILD-TYPE | 4 | 2 | 1 | 2 | 0 | 0 | 1 | 5

Figure S26. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0073

Table S27. Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
5P GAIN MUTATED | 7 | 10 | 14 | 18
5P GAIN WILD-TYPE | 17 | 3 | 3 | 5

Figure S27. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S28. Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
5P GAIN MUTATED | 6 | 18 | 3 | 22
5P GAIN WILD-TYPE | 17 | 5 | 4 | 2

Figure S28. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S29. Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
5Q GAIN MUTATED | 8 | 21 | 14 | 10
5Q GAIN WILD-TYPE | 28 | 5 | 2 | 2

Figure S29. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00836 (Fisher's exact test), Q value = 0.063

Table S30. Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
5Q GAIN MUTATED | 7 | 4 | 17 | 11 | 9
5Q GAIN WILD-TYPE | 11 | 7 | 3 | 7 | 2

Figure S30. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0073

Table S31. Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
5Q GAIN MUTATED | 7 | 10 | 15 | 15
5Q GAIN WILD-TYPE | 17 | 3 | 2 | 8

Figure S31. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S32. Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
5Q GAIN MUTATED | 5 | 19 | 3 | 20
5Q GAIN WILD-TYPE | 18 | 4 | 4 | 4

Figure S32. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.099

Table S33. Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
6P GAIN MUTATED | 7 | 1 | 5 | 5
6P GAIN WILD-TYPE | 29 | 25 | 11 | 7

Figure S33. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S34. Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
7P GAIN MUTATED | 8 | 20 | 12 | 8
7P GAIN WILD-TYPE | 28 | 6 | 4 | 4

Figure S34. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.0031

Table S35. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
7P GAIN MUTATED | 6 | 12 | 13 | 11
7P GAIN WILD-TYPE | 18 | 1 | 4 | 12

Figure S35. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00152 (Fisher's exact test), Q value = 0.017

Table S36. Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
7P GAIN MUTATED | 7 | 19 | 2 | 14
7P GAIN WILD-TYPE | 16 | 4 | 5 | 10

Figure S36. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00066

Table S37. Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
7Q GAIN MUTATED | 7 | 20 | 13 | 8
7Q GAIN WILD-TYPE | 29 | 6 | 3 | 4

Figure S37. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S38. Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
7Q GAIN MUTATED | 5 | 13 | 13 | 11
7Q GAIN WILD-TYPE | 19 | 0 | 4 | 12

Figure S38. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0025

Table S39. Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
7Q GAIN MUTATED | 6 | 20 | 2 | 14
7Q GAIN WILD-TYPE | 17 | 3 | 5 | 10

Figure S39. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S40. Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
8P GAIN MUTATED | 5 | 18 | 4 | 5
8P GAIN WILD-TYPE | 31 | 8 | 12 | 7

Figure S40. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0032

Table S41. Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
8Q GAIN MUTATED | 9 | 20 | 4 | 5
8Q GAIN WILD-TYPE | 27 | 6 | 12 | 7

Figure S41. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0019

Table S42. Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
9P GAIN MUTATED | 2 | 4 | 10 | 4
9P GAIN WILD-TYPE | 34 | 22 | 6 | 8

Figure S42. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.022

Table S43. Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
9P GAIN MUTATED | 2 | 5 | 8 | 0 | 1
9P GAIN WILD-TYPE | 16 | 6 | 12 | 18 | 10

Figure S43. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.078

Table S44. Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 21 | 24
9P GAIN MUTATED | 1 | 9
9P GAIN WILD-TYPE | 20 | 15

Figure S44. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00957 (Fisher's exact test), Q value = 0.069

Table S45. Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
9P GAIN MUTATED | 1 | 6 | 5 | 3
9P GAIN WILD-TYPE | 23 | 7 | 12 | 20

Figure S45. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.077

Table S46. Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
9P GAIN MUTATED | 3 | 10 | 0 | 2
9P GAIN WILD-TYPE | 20 | 13 | 7 | 22

Figure S46. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.0053

Table S47. Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
9Q GAIN MUTATED | 8 | 4 | 12 | 5
9Q GAIN WILD-TYPE | 28 | 22 | 4 | 7

Figure S47. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #1: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.013

Table S48. Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
9Q GAIN MUTATED | 8 | 5 | 9 | 0 | 1
9Q GAIN WILD-TYPE | 10 | 6 | 11 | 18 | 10

Figure S48. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 0.038

Table S49. Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 21 | 24
9Q GAIN MUTATED | 2 | 12
9Q GAIN WILD-TYPE | 19 | 12

Figure S49. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.12

Table S50. Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
9Q GAIN MUTATED | 6 | 8 | 5 | 3
9Q GAIN WILD-TYPE | 18 | 5 | 12 | 20

Figure S50. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.02

Table S51. Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
9Q GAIN MUTATED | 8 | 12 | 0 | 2
9Q GAIN WILD-TYPE | 15 | 11 | 7 | 22

Figure S51. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.15

Table S52. Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
9Q GAIN MUTATED | 13 | 7 | 3
9Q GAIN WILD-TYPE | 23 | 9 | 23

Figure S52. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.021

Table S53. Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
10P GAIN MUTATED | 7 | 5 | 11 | 2
10P GAIN WILD-TYPE | 29 | 21 | 5 | 10

Figure S53. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'CN_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.13

Table S54. Gene #19: '10p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 21 | 24
10P GAIN MUTATED | 3 | 11
10P GAIN WILD-TYPE | 18 | 13

Figure S54. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.087

Table S55. Gene #19: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
10P GAIN MUTATED | 6 | 3 | 0 | 2 | 1 | 1 | 0 | 1
10P GAIN WILD-TYPE | 2 | 4 | 7 | 1 | 3 | 3 | 6 | 5

Figure S55. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S56. Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
10P GAIN MUTATED | 6 | 11 | 4 | 2
10P GAIN WILD-TYPE | 18 | 2 | 13 | 21

Figure S56. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0038

Table S57. Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
10P GAIN MUTATED | 7 | 14 | 1 | 1
10P GAIN WILD-TYPE | 16 | 9 | 6 | 23

Figure S57. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.15

Table S58. Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
10P GAIN MUTATED | 13 | 7 | 3
10P GAIN WILD-TYPE | 23 | 9 | 23

Figure S58. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.017

Table S59. Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
10Q GAIN MUTATED | 9 | 5 | 11 | 1
10Q GAIN WILD-TYPE | 27 | 21 | 5 | 11

Figure S59. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'CN_CNMF'

'10q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.087

Table S60. Gene #20: '10q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
10Q GAIN MUTATED | 6 | 2 | 0 | 2 | 1 | 1 | 0 | 1
10Q GAIN WILD-TYPE | 2 | 5 | 7 | 1 | 3 | 3 | 6 | 5

Figure S60. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00095

Table S61. Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
10Q GAIN MUTATED | 7 | 11 | 3 | 2
10Q GAIN WILD-TYPE | 17 | 2 | 14 | 21

Figure S61. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0068

Table S62. Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
10Q GAIN MUTATED | 8 | 13 | 1 | 1
10Q GAIN WILD-TYPE | 15 | 10 | 6 | 23

Figure S62. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.11

Table S63. Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
10Q GAIN MUTATED | 12 | 8 | 3
10Q GAIN WILD-TYPE | 24 | 8 | 23

Figure S63. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.14

Table S64. Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
10Q GAIN MUTATED | 8 | 11 | 4
10Q GAIN WILD-TYPE | 20 | 11 | 23

Figure S64. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.18

Table S65. Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
11Q GAIN MUTATED | 4 | 0 | 0 | 0
11Q GAIN WILD-TYPE | 20 | 13 | 17 | 23

Figure S65. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00533 (Fisher's exact test), Q value = 0.044

Table S66. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
11Q GAIN MUTATED | 0 | 4 | 0
11Q GAIN WILD-TYPE | 28 | 18 | 27

Figure S66. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S67. Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
12P GAIN MUTATED | 14 | 26 | 15 | 9
12P GAIN WILD-TYPE | 22 | 0 | 1 | 3

Figure S67. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0028

Table S68. Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
12P GAIN MUTATED | 9 | 13 | 14 | 18
12P GAIN WILD-TYPE | 15 | 0 | 3 | 5

Figure S68. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0022

Table S69. Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
12P GAIN MUTATED | 10 | 20 | 2 | 22
12P GAIN WILD-TYPE | 13 | 3 | 5 | 2

Figure S69. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S70. Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
12Q GAIN MUTATED | 13 | 26 | 16 | 9
12Q GAIN WILD-TYPE | 23 | 0 | 0 | 3

Figure S70. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'CN_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.13

Table S71. Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
12Q GAIN MUTATED | 7 | 6 | 6 | 3 | 2 | 4 | 5 | 1
12Q GAIN WILD-TYPE | 1 | 1 | 1 | 0 | 2 | 0 | 1 | 5

Figure S71. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0079

Table S72. Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
12Q GAIN MUTATED | 10 | 13 | 14 | 18
12Q GAIN WILD-TYPE | 14 | 0 | 3 | 5

Figure S72. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0025

Table S73. Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
12Q GAIN MUTATED | 11 | 20 | 2 | 22
12Q GAIN WILD-TYPE | 12 | 3 | 5 | 2

Figure S73. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.17

Table S74. Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
13Q GAIN MUTATED | 1 | 1 | 4 | 0
13Q GAIN WILD-TYPE | 23 | 12 | 13 | 23

Figure S74. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'CN_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.088

Table S75. Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
14Q GAIN MUTATED | 6 | 4 | 9 | 2
14Q GAIN WILD-TYPE | 30 | 22 | 7 | 10

Figure S75. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #1: 'CN_CNMF'

'14q gain' versus 'RPPA_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.12

Table S76. Gene #26: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 21 | 24
14Q GAIN MUTATED | 1 | 8
14Q GAIN WILD-TYPE | 20 | 16

Figure S76. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0068

Table S77. Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
14Q GAIN MUTATED | 2 | 6 | 8 | 1
14Q GAIN WILD-TYPE | 22 | 7 | 9 | 22

Figure S77. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.013

Table S78. Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
14Q GAIN MUTATED | 3 | 12 | 0 | 2
14Q GAIN WILD-TYPE | 20 | 11 | 7 | 22

Figure S78. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S79. Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
14Q GAIN MUTATED | 17 | 0 | 1
14Q GAIN WILD-TYPE | 19 | 16 | 25

Figure S79. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0032

Table S80. Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
14Q GAIN MUTATED | 7 | 0 | 3 | 5 | 3
14Q GAIN WILD-TYPE | 9 | 27 | 8 | 15 | 1

Figure S80. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0015

Table S81. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
14Q GAIN MUTATED | 14 | 2 | 1
14Q GAIN WILD-TYPE | 14 | 20 | 26

Figure S81. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S82. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 39 | 24 | 14
14Q GAIN MUTATED | 17 | 0 | 0
14Q GAIN WILD-TYPE | 22 | 24 | 14

Figure S82. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.18

Table S83. Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
15Q GAIN MUTATED | 0 | 2 | 6 | 1 | 1
15Q GAIN WILD-TYPE | 18 | 9 | 14 | 17 | 10

Figure S83. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.076

Table S84. Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
15Q GAIN MUTATED | 0 | 3 | 5 | 2
15Q GAIN WILD-TYPE | 24 | 10 | 12 | 21

Figure S84. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.044

Table S85. Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
15Q GAIN MUTATED | 1 | 8 | 0 | 1
15Q GAIN WILD-TYPE | 22 | 15 | 7 | 23

Figure S85. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0081

Table S86. Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
15Q GAIN MUTATED | 6 | 1 | 1 | 0 | 2
15Q GAIN WILD-TYPE | 10 | 26 | 10 | 20 | 2

Figure S86. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S87. Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
16P GAIN MUTATED | 6 | 26 | 11 | 6
16P GAIN WILD-TYPE | 30 | 0 | 5 | 6

Figure S87. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.075

Table S88. Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
16P GAIN MUTATED | 4 | 6 | 16 | 10 | 6
16P GAIN WILD-TYPE | 14 | 5 | 4 | 8 | 5

Figure S88. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.038 (Fisher's exact test), Q value = 0.16

Table S89. Gene #28: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
16P GAIN MUTATED | 3 | 7 | 4 | 0 | 1 | 3 | 4 | 2
16P GAIN WILD-TYPE | 5 | 0 | 3 | 3 | 3 | 1 | 2 | 4

Figure S89. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S90. Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
16P GAIN MUTATED | 3 | 10 | 13 | 16
16P GAIN WILD-TYPE | 21 | 3 | 4 | 7

Figure S90. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S91. Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
16P GAIN MUTATED | 4 | 20 | 0 | 18
16P GAIN WILD-TYPE | 19 | 3 | 7 | 6

Figure S91. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.18

Table S92. Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
16P GAIN MUTATED | 17 | 6 | 19
16P GAIN WILD-TYPE | 19 | 10 | 7

Figure S92. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.13

Table S93. Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
16P GAIN MUTATED | 12 | 16 | 6 | 5 | 3
16P GAIN WILD-TYPE | 4 | 11 | 5 | 15 | 1

Figure S93. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.14

Table S94. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
16P GAIN MUTATED | 15 | 7 | 19
16P GAIN WILD-TYPE | 13 | 15 | 8

Figure S94. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S95. Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
16Q GAIN MUTATED | 5 | 25 | 11 | 6
16Q GAIN WILD-TYPE | 31 | 1 | 5 | 6

Figure S95. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 0.06

Table S96. Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
16Q GAIN MUTATED | 4 | 5 | 16 | 11 | 6
16Q GAIN WILD-TYPE | 14 | 6 | 4 | 7 | 5

Figure S96. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0024

Table S97. Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
16Q GAIN MUTATED | 4 | 9 | 13 | 16
16Q GAIN WILD-TYPE | 20 | 4 | 4 | 7

Figure S97. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S98. Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
16Q GAIN MUTATED | 4 | 19 | 1 | 18
16Q GAIN WILD-TYPE | 19 | 4 | 6 | 6

Figure S98. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.12

Table S99. Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
16Q GAIN MUTATED | 18 | 5 | 19
16Q GAIN WILD-TYPE | 18 | 11 | 7

Figure S99. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.013 (Fisher's exact test), Q value = 0.085

Table S100. Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
16Q GAIN MUTATED | 13 | 16 | 6 | 5 | 2
16Q GAIN WILD-TYPE | 3 | 11 | 5 | 15 | 2

Figure S100. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.087

Table S101. Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
16Q GAIN MUTATED | 17 | 6 | 18
16Q GAIN WILD-TYPE | 11 | 16 | 9

Figure S101. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 0.0244 (Fisher's exact test), Q value = 0.12

Table S102. Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
17Q GAIN MUTATED | 4 | 0 | 0 | 3
17Q GAIN WILD-TYPE | 32 | 26 | 16 | 9

Figure S102. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'CN_CNMF'

P value = 0.00373 (Fisher's exact test), Q value = 0.034

Table S103. Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
19P GAIN MUTATED | 16 | 16 | 15 | 9
19P GAIN WILD-TYPE | 20 | 10 | 1 | 3

Figure S103. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'CN_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.1

Table S104. Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
19P GAIN MUTATED | 8 | 7 | 4 | 2 | 1 | 3 | 4 | 2
19P GAIN WILD-TYPE | 0 | 0 | 3 | 1 | 3 | 1 | 2 | 4

Figure S104. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.014

Table S105. Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
19P GAIN MUTATED | 11 | 13 | 13 | 11
19P GAIN WILD-TYPE | 13 | 0 | 4 | 12

Figure S105. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.0072

Table S106. Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
19P GAIN MUTATED | 14 | 21 | 1 | 12
19P GAIN WILD-TYPE | 9 | 2 | 6 | 12

Figure S106. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0015

Table S107. Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
19Q GAIN MUTATED | 13 | 16 | 16 | 7
19Q GAIN WILD-TYPE | 23 | 10 | 0 | 5

Figure S107. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 0.05 (Fisher's exact test), Q value = 0.19

Table S108. Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
19Q GAIN MUTATED | 12 | 6 | 16 | 7 | 4
19Q GAIN WILD-TYPE | 6 | 5 | 4 | 11 | 7

Figure S108. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.0057

Table S109. Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
19Q GAIN MUTATED | 10 | 13 | 12 | 9
19Q GAIN WILD-TYPE | 14 | 0 | 5 | 14

Figure S109. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.013

Table S110. Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
19Q GAIN MUTATED | 12 | 20 | 1 | 11
19Q GAIN WILD-TYPE | 11 | 3 | 6 | 13

Figure S110. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S111. Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
20P GAIN MUTATED | 6 | 22 | 11 | 7
20P GAIN WILD-TYPE | 30 | 4 | 5 | 5

Figure S111. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.027

Table S112. Gene #36: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 21 | 24
20P GAIN MUTATED | 16 | 7
20P GAIN WILD-TYPE | 5 | 17

Figure S112. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00853 (Fisher's exact test), Q value = 0.064

Table S113. Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
20P GAIN MUTATED | 5 | 2 | 6 | 1 | 1 | 4 | 4 | 0
20P GAIN WILD-TYPE | 3 | 5 | 1 | 2 | 3 | 0 | 2 | 6

Figure S113. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0032

Table S114. Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
20P GAIN MUTATED | 4 | 9 | 8 | 18
20P GAIN WILD-TYPE | 20 | 4 | 9 | 5

Figure S114. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.0022

Table S115. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
20P GAIN MUTATED | 6 | 12 | 1 | 20
20P GAIN WILD-TYPE | 17 | 11 | 6 | 4

Figure S115. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.041

Table S116. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
20P GAIN MUTATED | 13 | 7 | 20
20P GAIN WILD-TYPE | 23 | 9 | 6

Figure S116. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00945 (Fisher's exact test), Q value = 0.069

Table S117. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
20P GAIN MUTATED | 10 | 9 | 20
20P GAIN WILD-TYPE | 18 | 13 | 7

Figure S117. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00408 (Fisher's exact test), Q value = 0.037

Table S118. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 39 | 24 | 14
20P GAIN MUTATED | 13 | 18 | 8
20P GAIN WILD-TYPE | 26 | 6 | 6

Figure S118. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S119. Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
20Q GAIN MUTATED | 8 | 22 | 12 | 7
20Q GAIN WILD-TYPE | 28 | 4 | 4 | 5

Figure S119. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.092

Table S120. Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 21 | 24
20Q GAIN MUTATED | 16 | 9
20Q GAIN WILD-TYPE | 5 | 15

Figure S120. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.0017

Table S121. Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
20Q GAIN MUTATED | 5 | 11 | 8 | 18
20Q GAIN WILD-TYPE | 19 | 2 | 9 | 5

Figure S121. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.0051

Table S122. Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
20Q GAIN MUTATED | 6 | 14 | 2 | 20
20Q GAIN WILD-TYPE | 17 | 9 | 5 | 4

Figure S122. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.1

Table S123. Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
20Q GAIN MUTATED | 15 | 8 | 20
20Q GAIN WILD-TYPE | 21 | 8 | 6

Figure S123. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.078

Table S124. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
20Q GAIN MUTATED | 12 | 9 | 21
20Q GAIN WILD-TYPE | 16 | 13 | 6

Figure S124. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.087

Table S125. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 39 | 24 | 14
20Q GAIN MUTATED | 15 | 18 | 9
20Q GAIN WILD-TYPE | 24 | 6 | 5

Figure S125. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.11

Table S126. Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
21Q GAIN MUTATED | 9 | 8 | 11 | 3
21Q GAIN WILD-TYPE | 27 | 18 | 5 | 9

Figure S126. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00789 (Fisher's exact test), Q value = 0.06

Table S127. Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
21Q GAIN MUTATED | 8 | 2 | 12 | 2 | 2
21Q GAIN WILD-TYPE | 10 | 9 | 8 | 16 | 9

Figure S127. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.1

Table S128. Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
21Q GAIN MUTATED | 7 | 9 | 6 | 4
21Q GAIN WILD-TYPE | 17 | 4 | 11 | 19

Figure S128. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.013

Table S129. Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
21Q GAIN MUTATED | 7 | 15 | 1 | 3
21Q GAIN WILD-TYPE | 16 | 8 | 6 | 21

Figure S129. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.085

Table S130. Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
21Q GAIN MUTATED | 18 | 4 | 4
21Q GAIN WILD-TYPE | 18 | 12 | 22

Figure S130. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0204 (Fisher's exact test), Q value = 0.11

Table S131. Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
21Q GAIN MUTATED | 10 | 4 | 4 | 6 | 2
21Q GAIN WILD-TYPE | 6 | 23 | 7 | 14 | 2

Figure S131. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.027

Table S132. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
21Q GAIN MUTATED | 15 | 7 | 3
21Q GAIN WILD-TYPE | 13 | 15 | 24

Figure S132. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00039

Table S133. Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
XP GAIN MUTATED | 6 | 22 | 9 | 5
XP GAIN WILD-TYPE | 30 | 4 | 7 | 7

Figure S133. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'CN_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.14

Table S134. Gene #40: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
XP GAIN MUTATED | 6 | 5 | 5 | 0 | 2 | 3 | 4 | 0
XP GAIN WILD-TYPE | 2 | 2 | 2 | 3 | 2 | 1 | 2 | 6

Figure S134. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.013

Table S135. Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
XP GAIN MUTATED | 4 | 10 | 11 | 12
XP GAIN WILD-TYPE | 20 | 3 | 6 | 11

Figure S135. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00536 (Fisher's exact test), Q value = 0.044

Table S136. Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
XP GAIN MUTATED | 5 | 14 | 2 | 16
XP GAIN WILD-TYPE | 18 | 9 | 5 | 8

Figure S136. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00066

Table S137. Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
XQ GAIN MUTATED | 7 | 21 | 8 | 5
XQ GAIN WILD-TYPE | 29 | 5 | 8 | 7

Figure S137. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.18

Table S138. Gene #41: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
XQ GAIN MUTATED | 6 | 4 | 5 | 0 | 2 | 3 | 4 | 0
XQ GAIN WILD-TYPE | 2 | 3 | 2 | 3 | 2 | 1 | 2 | 6

Figure S138. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.015

Table S139. Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
XQ GAIN MUTATED | 4 | 10 | 10 | 12
XQ GAIN WILD-TYPE | 20 | 3 | 7 | 11

Figure S139. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00877 (Fisher's exact test), Q value = 0.065

Table S140. Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
XQ GAIN MUTATED | 5 | 13 | 2 | 16
XQ GAIN WILD-TYPE | 18 | 10 | 5 | 8

Figure S140. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.13

Table S141. Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
1P LOSS MUTATED | 4 | 10 | 11
1P LOSS WILD-TYPE | 24 | 12 | 16

Figure S141. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.12

Table S142. Gene #43: '1q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
1Q LOSS MUTATED | 0 | 0 | 0 | 2 | 1 | 0 | 2 | 2
1Q LOSS WILD-TYPE | 8 | 7 | 7 | 1 | 3 | 4 | 4 | 4

Figure S142. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00684 (Fisher's exact test), Q value = 0.054

Table S143. Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
2P LOSS MUTATED | 4 | 2 | 5 | 6
2P LOSS WILD-TYPE | 32 | 24 | 11 | 6

Figure S143. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.13

Table S144. Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
2P LOSS MUTATED | 1 | 1 | 7 | 2 | 5
2P LOSS WILD-TYPE | 17 | 10 | 13 | 16 | 6

Figure S144. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 0.0381 (Fisher's exact test), Q value = 0.16

Table S145. Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
2P LOSS MUTATED | 8 | 0 | 8
2P LOSS WILD-TYPE | 28 | 16 | 18

Figure S145. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 0.00495 (Fisher's exact test), Q value = 0.041

Table S146. Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
2Q LOSS MUTATED | 3 | 2 | 4 | 6
2Q LOSS WILD-TYPE | 33 | 24 | 12 | 6

Figure S146. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.014

Table S147. Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
2Q LOSS MUTATED | 0 | 0 | 7 | 2 | 5
2Q LOSS WILD-TYPE | 18 | 11 | 13 | 16 | 6

Figure S147. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.14

Table S148. Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
2Q LOSS MUTATED | 6 | 0 | 8
2Q LOSS WILD-TYPE | 30 | 16 | 18

Figure S148. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 0.12

Table S149. Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
3Q LOSS MUTATED | 7 | 0 | 7 | 3
3Q LOSS WILD-TYPE | 17 | 13 | 10 | 20

Figure S149. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.14

Table S150. Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
3Q LOSS MUTATED | 8 | 7 | 1 | 1
3Q LOSS WILD-TYPE | 15 | 16 | 6 | 23

Figure S150. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.12

Table S151. Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
4P LOSS MUTATED | 7 | 0 | 1 | 1
4P LOSS WILD-TYPE | 17 | 13 | 16 | 22

Figure S151. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 0.00756 (Fisher's exact test), Q value = 0.058

Table S152. Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
4Q LOSS MUTATED | 8 | 0 | 1 | 1
4Q LOSS WILD-TYPE | 16 | 13 | 16 | 22

Figure S152. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0267 (Fisher's exact test), Q value = 0.13

Table S153. Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
4Q LOSS MUTATED | 7 | 1 | 1 | 1
4Q LOSS WILD-TYPE | 16 | 22 | 6 | 23

Figure S153. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.085

Table S154. Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
4Q LOSS MUTATED | 2 | 7 | 1
4Q LOSS WILD-TYPE | 26 | 15 | 26

Figure S154. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.071

Table S155. Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
5P LOSS MUTATED | 6 | 1 | 0 | 0
5P LOSS WILD-TYPE | 17 | 22 | 7 | 24

Figure S155. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 0.00535 (Fisher's exact test), Q value = 0.044

Table S156. Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
8P LOSS MUTATED | 8 | 0 | 6 | 2
8P LOSS WILD-TYPE | 28 | 26 | 10 | 10

Figure S156. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'CN_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.0075

Table S157. Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
8P LOSS MUTATED | 1 | 1 | 0 | 2 | 0 | 0 | 0 | 5
8P LOSS WILD-TYPE | 7 | 6 | 7 | 1 | 4 | 4 | 6 | 1

Figure S157. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.12

Table S158. Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
8P LOSS MUTATED | 2 | 2 | 1 | 5 | 3
8P LOSS WILD-TYPE | 14 | 25 | 10 | 15 | 1

Figure S158. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.14

Table S159. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 39 | 24 | 14
8P LOSS MUTATED | 11 | 1 | 1
8P LOSS WILD-TYPE | 28 | 23 | 13

Figure S159. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 0.00484 (Fisher's exact test), Q value = 0.041

Table S160. Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
8Q LOSS MUTATED | 4 | 0 | 6 | 2
8Q LOSS WILD-TYPE | 32 | 26 | 10 | 10

Figure S160. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #1: 'CN_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 0.16

Table S161. Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
8Q LOSS MUTATED | 1 | 1 | 0 | 2 | 0 | 0 | 0 | 3
8Q LOSS WILD-TYPE | 7 | 6 | 7 | 1 | 4 | 4 | 6 | 3

Figure S161. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.15

Table S162. Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
8Q LOSS MUTATED | 3 | 2 | 5 | 0
8Q LOSS WILD-TYPE | 21 | 11 | 12 | 23

Figure S162. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0342 (Fisher's exact test), Q value = 0.15

Table S163. Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
8Q LOSS MUTATED | 1 | 1 | 1 | 5 | 2
8Q LOSS WILD-TYPE | 15 | 26 | 10 | 15 | 2

Figure S163. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.16

Table S164. Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 39 | 24 | 14
8Q LOSS MUTATED | 9 | 1 | 0
8Q LOSS WILD-TYPE | 30 | 23 | 14

Figure S164. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.018

Table S165. Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
9P LOSS MUTATED | 15 | 2 | 3 | 0
9P LOSS WILD-TYPE | 21 | 24 | 13 | 12

Figure S165. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.19

Table S166. Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
9P LOSS MUTATED | 9 | 3 | 2 | 4 | 1
9P LOSS WILD-TYPE | 9 | 8 | 18 | 14 | 10

Figure S166. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0022

Table S167. Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
9P LOSS MUTATED | 14 | 1 | 3 | 1
9P LOSS WILD-TYPE | 10 | 12 | 14 | 22

Figure S167. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.013

Table S168. Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
9P LOSS MUTATED | 12 | 4 | 2 | 1
9P LOSS WILD-TYPE | 11 | 19 | 5 | 23

Figure S168. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 0.00931 (Fisher's exact test), Q value = 0.068

Table S169. Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
9P LOSS MUTATED | 9 | 8 | 2
9P LOSS WILD-TYPE | 27 | 8 | 24

Figure S169. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00431 (Fisher's exact test), Q value = 0.038

Table S170. Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
9P LOSS MUTATED | 4 | 11 | 3
9P LOSS WILD-TYPE | 24 | 11 | 24

Figure S170. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.16

Table S171. Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
9Q LOSS MUTATED | 0 | 0 | 0 | 0 | 1 | 0 | 3 | 1
9Q LOSS WILD-TYPE | 8 | 7 | 7 | 3 | 3 | 4 | 3 | 5

Figure S171. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 0.00649 (Fisher's exact test), Q value = 0.052

Table S172. Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
11P LOSS MUTATED | 7 | 3 | 7 | 7
11P LOSS WILD-TYPE | 29 | 23 | 9 | 5

Figure S172. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.099

Table S173. Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
11P LOSS MUTATED | 4 | 1 | 11 | 2 | 4
11P LOSS WILD-TYPE | 14 | 10 | 9 | 16 | 7

Figure S173. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q loss' versus 'CN_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.08

Table S174. Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
11Q LOSS MUTATED | 7 | 3 | 6 | 7
11Q LOSS WILD-TYPE | 29 | 23 | 10 | 5

Figure S174. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #1: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.029

Table S175. Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
11Q LOSS MUTATED | 2 | 1 | 11 | 2 | 5
11Q LOSS WILD-TYPE | 16 | 10 | 9 | 16 | 6

Figure S175. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.16

Table S176. Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
12P LOSS MUTATED | 2 | 1 | 2 | 0
12P LOSS WILD-TYPE | 21 | 22 | 5 | 24

Figure S176. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'METHLYATION_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.19

Table S177. Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
12Q LOSS MUTATED | 0 | 2 | 0 | 2 | 0
12Q LOSS WILD-TYPE | 18 | 9 | 20 | 16 | 11

Figure S177. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00999 (Fisher's exact test), Q value = 0.071

Table S178. Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
12Q LOSS MUTATED | 2 | 0 | 2 | 0
12Q LOSS WILD-TYPE | 21 | 23 | 5 | 24

Figure S178. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.087

Table S179. Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
13Q LOSS MUTATED | 19 | 5 | 7 | 8
13Q LOSS WILD-TYPE | 17 | 21 | 9 | 4

Figure S179. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.13

Table S180. Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
14Q LOSS MUTATED | 8 | 3 | 1 | 6
14Q LOSS WILD-TYPE | 28 | 23 | 15 | 6

Figure S180. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.099

Table S181. Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
14Q LOSS MUTATED | 7 | 0 | 1 | 8
14Q LOSS WILD-TYPE | 17 | 13 | 16 | 15

Figure S181. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.19

Table S182. Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
14Q LOSS MUTATED | 5 | 1 | 3 | 7
14Q LOSS WILD-TYPE | 18 | 22 | 4 | 17

Figure S182. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0401 (Fisher's exact test), Q value = 0.17

Table S183. Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
15Q LOSS MUTATED | 0 | 7 | 2 | 8 | 1
15Q LOSS WILD-TYPE | 16 | 20 | 9 | 12 | 3

Figure S183. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.19

Table S184. Gene #69: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5 | CLUS_6 | CLUS_7 | CLUS_8
--- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 8 | 7 | 7 | 3 | 4 | 4 | 6 | 6
16P LOSS MUTATED | 2 | 0 | 0 | 1 | 2 | 0 | 0 | 0
16P LOSS WILD-TYPE | 6 | 7 | 7 | 2 | 2 | 4 | 6 | 6

Figure S184. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.022

Table S185. Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
16P LOSS MUTATED | 6 | 0 | 0 | 0
16P LOSS WILD-TYPE | 18 | 13 | 17 | 23

Figure S185. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00431 (Fisher's exact test), Q value = 0.038

Table S186. Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
16P LOSS MUTATED | 4 | 0 | 2 | 0
16P LOSS WILD-TYPE | 19 | 23 | 5 | 24

Figure S186. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.085

Table S187. Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 36 | 16 | 26
16P LOSS MUTATED | 2 | 4 | 0
16P LOSS WILD-TYPE | 34 | 12 | 26

Figure S187. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.0049

Table S188. Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
16P LOSS MUTATED | 0 | 6 | 0
16P LOSS WILD-TYPE | 28 | 16 | 27

Figure S188. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00152 (Fisher's exact test), Q value = 0.017

Table S189. Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
16Q LOSS MUTATED | 0 | 5 | 0
16Q LOSS WILD-TYPE | 28 | 17 | 27

Figure S189. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'CN_CNMF'

P value = 0.00278 (Fisher's exact test), Q value = 0.027

Table S190. Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
17P LOSS MUTATED | 16 | 3 | 10 | 3
17P LOSS WILD-TYPE | 20 | 23 | 6 | 9

Figure S190. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.0032

Table S191. Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
17P LOSS MUTATED | 11 | 0 | 12 | 4 | 1
17P LOSS WILD-TYPE | 7 | 11 | 8 | 14 | 10

Figure S191. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.076

Table S192. Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
17P LOSS MUTATED | 14 | 4 | 7 | 3
17P LOSS WILD-TYPE | 10 | 9 | 10 | 20

Figure S192. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.086

Table S193. Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
17P LOSS MUTATED | 12 | 11 | 2 | 3
17P LOSS WILD-TYPE | 11 | 12 | 5 | 21

Figure S193. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0028 (Fisher's exact test), Q value = 0.027

Table S194. Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
17P LOSS MUTATED | 5 | 8 | 0 | 13 | 2
17P LOSS WILD-TYPE | 11 | 19 | 11 | 7 | 2

Figure S194. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.085

Table S195. Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
17P LOSS MUTATED | 9 | 13 | 5
17P LOSS WILD-TYPE | 19 | 9 | 22

Figure S195. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'CN_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.088

Table S196. Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
17Q LOSS MUTATED | 10 | 3 | 9 | 2
17Q LOSS WILD-TYPE | 26 | 23 | 7 | 10

Figure S196. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 0.00483 (Fisher's exact test), Q value = 0.041

Table S197. Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 18 | 11 | 20 | 18 | 11
17Q LOSS MUTATED | 7 | 1 | 12 | 3 | 1
17Q LOSS WILD-TYPE | 11 | 10 | 8 | 15 | 10

Figure S197. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.15

Table S198. Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
17Q LOSS MUTATED | 9 | 11 | 1 | 3
17Q LOSS WILD-TYPE | 14 | 12 | 6 | 21

Figure S198. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.11

Table S199. Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 | CLUS_5
--- | --- | --- | --- | --- | ---
ALL | 16 | 27 | 11 | 20 | 4
17Q LOSS MUTATED | 6 | 6 | 0 | 10 | 2
17Q LOSS WILD-TYPE | 10 | 21 | 11 | 10 | 2

Figure S199. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.12

Table S200. Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
18P LOSS MUTATED | 16 | 5 | 8 | 8
18P LOSS WILD-TYPE | 20 | 21 | 8 | 4

Figure S200. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'CN_CNMF'

'18q loss' versus 'CN_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.16

Table S201. Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
18Q LOSS MUTATED | 15 | 5 | 7 | 8
18Q LOSS WILD-TYPE | 21 | 21 | 9 | 4

Figure S201. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'CN_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.087

Table S202. Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
19P LOSS MUTATED | 1 | 0 | 2 | 0
19P LOSS WILD-TYPE | 22 | 23 | 5 | 24

Figure S202. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.17

Table S203. Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
20P LOSS MUTATED | 6 | 0 | 3 | 0
20P LOSS WILD-TYPE | 30 | 26 | 13 | 12

Figure S203. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'CN_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.11

Table S204. Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 22 | 27
20P LOSS MUTATED | 2 | 5 | 0
20P LOSS WILD-TYPE | 26 | 17 | 27

Figure S204. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.087

Table S205. Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
22Q LOSS MUTATED | 22 | 7 | 11 | 8
22Q LOSS WILD-TYPE | 14 | 19 | 5 | 4

Figure S205. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S206. Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
XP LOSS MUTATED | 14 | 0 | 0 | 2
XP LOSS WILD-TYPE | 22 | 26 | 16 | 10

Figure S206. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'CN_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.12

Table S207. Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
XP LOSS MUTATED | 9 | 0 | 2 | 3
XP LOSS WILD-TYPE | 15 | 13 | 15 | 20

Figure S207. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.13

Table S208. Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
XP LOSS MUTATED | 9 | 2 | 1 | 2
XP LOSS WILD-TYPE | 14 | 21 | 6 | 22

Figure S208. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.027

Table S209. Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 36 | 26 | 16 | 12
XQ LOSS MUTATED | 12 | 1 | 0 | 2
XQ LOSS WILD-TYPE | 24 | 25 | 16 | 10

Figure S209. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.099

Table S210. Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 24 | 13 | 17 | 23
XQ LOSS MUTATED | 9 | 0 | 3 | 2
XQ LOSS WILD-TYPE | 15 | 13 | 14 | 21

Figure S210. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.096

Table S211. Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 23 | 23 | 7 | 24
XQ LOSS MUTATED | 9 | 3 | 1 | 1
XQ LOSS WILD-TYPE | 14 | 20 | 6 | 23

Figure S211. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

- Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

- Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/15081747/transformed.cor.cli.txt

- Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ACC-TP/15087341/ACC-TP.transferedmergedcluster.txt

- Number of patients = 90

- Number of significantly arm-level cnvs = 82

- Number of molecular subtypes = 10

- Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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